Document Type

Honors Project

First Advisor

Dr. Stephen Baron

Degree Award Date

Spring 4-30-2022


Staphylococcus aureus, Pseudomonas aeruginosa, longitudinal isolates, pangenome, panallelome


Bacteriology | Medical Microbiology | Pathogenic Microbiology


Cystic fibrosis (CF) is a progressive, genetic disease characterized by mutations in the CF transmembrane conductance regulator (CFTR) gene. When this gene’s function is compromised, mucus accumulates in the respiratory tracts, creating a breeding ground for chronic bacterial lung infections. Staphylococcus aureus and Pseudomonas aeruginosa are the two most frequently detected bacterial pathogens in the lungs of individuals who have CF. S. aureus is a Gram-positive, non-motile, sphere-shaped bacteria that causes pneumonia, endocarditis, as well as skin infections. P. aeruginosa is a Gram-negative, rod-shaped bacteria that is motile by means of a single polar flagellum. P. aeruginosa can cause UTIs, dermatitis, as well as respiratory system infections. These bacteria are opportunistic pathogens, meaning that they can be found in an individual’s normal flora, but they can cause infections in open wounds and respiratory tracts among other infections. Coinfections with these two pathogens leads to significantly worse patient prognosis, which is why it is imperative to determine how these two bacterial species adapt in the CF lung environment. Since P. aeruginosa and S. aureus are involved in polymicrobial interactions in coinfections, we hypothesized that clinical isolates from coinfections would have genetic changes involved in interactions compared to those that were monoisolated. The goal of this study was the develop a pipeline to analyze longitudinal clinical isolates for genetic adaptations. Whole genome sequencing was performed on S. aureus and P. aeruginosa clinical isolates from two patients. Genomes were assembled and annotated for further analysis to define longitudinal isolate relatedness, antibiotic resistance gene presence, and pangenomic and panallelome queries. To determine the relationship among the isolates, phylogenetic trees were constructed and strains were subjected to multi-locus sequencing typing. Several strains appeared to be longitudinal isolates from related lineages from each patient, while some were unrelated. The S. aureus strains were analyzed by additional genotyping based on staphylococcal-specific genes which revealed additional relatedness among the isolates. Next, the genomes were analyzed for antibiotic resistance genes. The results from these two patients suggested that lineages from persistent infections have more antibiotic resistance genes than the unrelated isolates. Genome presence-absence variation was defined and panallelome analysis identified rare alleles for each isolate. In summary, we developed a pipeline to identify pathways involved in adaptation during long-lasting coinfections in CF. Future studies will focus on deciphering the patterns in pangenomic and panallelome results to identify targets that can disrupt persistent infections.

Recommended Citation

Witmer, Lauren. "Defining Genetic Adaptations in Clinical Bacterial Isolates from Cystic Fibrosis.” Senior Honors Projects, Bridgewater College, 2021.